Aim:: Congenital Malformations (CMs) represent a challenge especially for developing countries. Data about CMs in Albania are rather scarce. In this context, our aim was to assess the prevalence and factors associated with CMs in Tirana, the capital of Albania. Methods:: Information on all CMs at birth during 2011-2013 was retrieved from the National CM Surveillance System. For each CM case, three controls (babies born without CM) were retrieved as well. Overall, 831 cases and 2522 controls were included in this study. The prevalence was calculated using the total number of live births in Tirana during the same period. Binary logistic regression was used to determine the factors associated with CMs adjusting for a number of covariates. Results:: The three-year prevalence of CMs was 23.41 per 1,000 live births. The most affected body systems were the musculoskeletal, cardiovascular and genital systems. CMs were more prevalent among male babies. Advanced mothers’ age, lower education, unemployment status and lower gestational age were all positively associated with increased likelihood of CMs. Conclusions:: Socio-demographic factors of mothers are linked to CMs in Albania. Future surveys are needed in Albania in order to establish determinants of CMs at a national level.